KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Chemicals, peptides, and recombinant proteins | ||
|
| ||
| TRIzol | Thermo Fisher Scientific | 15-596-018 |
| Phenol: chloroform: iso-amyl alcohol (25:24:1) | VWR | VWRV0966-100ML |
| PMSG | Lee BioSolutions | 493-10 |
| Collagenase | Sigma-Aldrich | C9407 |
| M2 media | Sigma-Aldrich | M7167 |
| HCG | Sigma-Aldrich | C1063 |
| Hyaluronidase | Sigma-Aldrich | H4272 |
| Sodium acetate buffer solution | Sigma-Aldrich | S7899 |
| GenElute LPA | Sigma-Aldrich | 56575 |
| DMEM media | Thermo Fisher Scientific | 11995073 |
| FBS | Cytiva | SH30071.03HI |
| Penicillin/Streptomycin | Thermo Fisher Scientific | 15140122 |
| 0.25% Trypsin-EDTA | Thermo Fisher Scientific | 25200114 |
|
| ||
| Critical commercial assays | ||
|
| ||
| PCR-cDNA Sequencing Kit | Oxford Nanopore Technologies | SQK-PCS110 |
| PCR-cDNA Barcoding Kit | Oxford Nanopore Technologies | SQK-PCB109 |
| R9.4.1 flow cell | Oxford Nanopore Technologies | FLO-MIN106D |
| Minion sequencing device | Oxford Nanopore Technologies | MIN-101B |
| AMPure XP | Beckman Coulter | A63881 |
| RNA Clean & Concentrator-5 | Zymo Research | R1014 |
| DNAse I | Zymo Research | E1011-A |
| T4 DNA Ligase | NEB | M0202M |
| 5x quick ligation reaction buffer | NEB | E6058A |
| Lambda exonuclease | NEB | M0262S |
| USER Enzyme | NEB | M5505S |
| RNAClean XP | Beckman Coulter | A63987 |
| Maxima H Minus Reverse Transcriptase | Thermo Fisher Scientific | EP0751 |
| dNTP Mix | NEB | N0447S |
| LongAmp Hot Start Taq 2x Master Mix | NEB | M0533S |
| Exonuclease I | NEB | M0293S |
| RNaseOUT | Thermo Fisher Scientific | 10777019 |
| RNA 6000 Pico Kit | Agilent Technologies | 5067-1513 |
| High Sensitivity DNA Kit | Agilent Technologies | 5067-4626 |
|
| ||
| Deposited data | ||
|
| ||
| Nanopore PCR-cDNA sequencing | This paper | GEO: GSE228001 |
| RNA-seq | Zhang et al.84 | GEO: GSE71434 |
| Ribosome profiling and RNA-seq | Xiong et al.62 | GEO: GSE165782 |
| RNA-seq | Zhang et al.64 | GEO: GSE169632 |
|
| ||
| Experimental models: Cell lines | ||
|
| ||
| Hela | ATCC | CCL-2 |
|
| ||
| Experimental models: Organisms/strains | ||
|
| ||
| C57B/6J mice | Jackson Labs | 000664 |
| B6D2F1/J mice | Jackson Labs | 100006 |
|
| ||
| Oligonucleotides | ||
|
| ||
| Polyadenylated standards (See method details for sequences) | This study | N/A |
|
| ||
| Software and algorithms | ||
|
| ||
| Minknow (22.05.5) | Oxford Nanopore Technologies | https://community.nanoporetech.com/downloads |
| Guppy (6.0.6) | Oxford Nanopore Technologies | https://community.nanoporetech.com/downloads |
| Pychopper (2.5.0) | Oxford Nanopore Technologies | https://github.com/epi2me-labs/pychopper |
| minimap2 (2.17) | Li et al.108 | https://github.com/lh3/minimap2 |
| Salmon (0.14.1) | Patro et al.109 | https://github.com/COMBINE-lab/salmon |
| tailfindr (1.3) | Krause et al.65 | https://github.com/adnaniazi/tailfindr |
| DESeq2 (1.34.0) | Love et al.110 | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| AME (5.0.2) | McLeay et al.111 | https://meme-suite.org/meme/tools/ame |
| clusterProfiler (4.2.2) | Yu et al.112 | https://bioconductor.org/packages/release/bioc/html/clusterProfiler.html |
|
| ||
| Other | ||
|
| ||
| ERCC Spike-In RNAs | Thermo Fisher Scientific | 4456653 |